PET117

PET117 cytochrome c oxidase chaperone, the group of Mitochondrial respiratory chain complex assembly factors

Basic information

Region (hg38): 20:18137863-18143169

Links

ENSG00000232838 ∙ NCBI:100303755 ∙ OMIM:614771 ∙ HGNC:40045 ∙ Uniprot:Q6UWS5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cytochrome-c oxidase deficiency disease (Supportive), mode of inheritance: AR
• mitochondrial complex 4 deficiency, nuclear type 19 (Limited), mode of inheritance: Unknown
• Leigh syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mitochondrial complex IV deficiency, nuclear type 19	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Biochemical; Neurologic	28386624

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PET117 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PET117 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			5		1	6
nonsense		1				1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	1	6	2	1

Variants in PET117

This is a list of pathogenic ClinVar variants found in the PET117 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
20-18137961-T-C		PET117-related disorder	Likely benign (Dec 06, 2023)
20-18137986-C-T		not specified	Uncertain significance (Feb 16, 2023)
20-18138018-C-T			Likely benign (Feb 01, 2024)
20-18142215-G-C		not specified	Uncertain significance (Aug 22, 2023)
20-18142250-C-T		not specified	Uncertain significance (Jun 22, 2021)
20-18142268-C-G			Benign (Feb 01, 2018)
20-18142268-C-T		not specified	Uncertain significance (Nov 08, 2021)
20-18142283-C-T		Mitochondrial complex 4 deficiency, nuclear type 19	Likely pathogenic (Dec 04, 2020)
20-18142319-G-A		not specified	Uncertain significance (Feb 06, 2023)
20-18142913-C-T			Uncertain significance (Aug 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PET117	protein_coding	protein_coding	ENST00000432901	2	5297

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0321	0.623	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.469	28	35.9	0.780	0.00000207	510
Missense in Polyphen		8	11.99	0.66721		152
Synonymous	-0.808	16	12.4	1.29	6.44e-7	161
Loss of Function	0.259	2	2.44	0.821	1.04e-7	36

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0907

Intolerance Scores

• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.04

Haploinsufficiency Scores

• pHI: 0.122
• hipred: N
• hipred_score: 0.352

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pet117

Gene ontology

• Biological process: mitochondrial respiratory chain complex IV assembly
• Cellular component: mitochondrion